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Open-source Software for Large-scale, High-throughput 3D Video Tracking of Bats

Aaron J. CorcoranAssistant Professor

Department of Biology

UC Colorado Springs

Presentation availablewww.sonarjamming.com

@AaronJCorcoran

Tyson L. Hedrick

Professor

Biology Department

University of North Carolina

Michael S. Schirmacher

Director

Wind Energy Program

Bat Conservation International

Image: Nickolay Hristov

Contexts for 3D tracking

Images: N. HristovA. CorcoranM. Schirmacher

3D Video tracking

Radar

On-board GPS

Videography

• High accuracy

• Behavioral detail

• Site-specific

Image: N. Hristov

You can track bats in 3D!!!

Use nearly any camera setup

User-friendly software

No software licenses required

Overview of 3D tracking

1. Video acquisition 3. 3D reconstruction2. Camera Calibration

What kind of cameras?How many cameras?Synchronization

What kind of cameras?

Near infrared

• Less expensive

• Need IR lights

• Flexible camera options

Thermal/far infrared• More expensive• No lights• Greater operating range

Images: Paul Colley (Left), Nick Hristov (right)

Video Acquisition

2 Camera setup 3 Camera setup

Increased accuracy

Multi-object tracking

Camera Synchronization

Cabled Sync• Frame-synced images

• Specialized cameras

• May require specialized acquisition software (e.g., Streampix)

Digital Signal generator

Camera Synchronization

Audio Sync• Images not frame synced

• Synced in software• 1/44100 second accuracy

• Interpolate tracked XY points

Audio signal(Bat chirp)

Jackson et al. 2016 Biology Open

Camera Calibration

Intrinsics

- Focal length/sensor size

- Lens distortion

Camera Calibration

Intrinsics

- Focal length/sensor size

- Lens distortion

Field calibration:camera positions & orientations

EasyWand

Theriault et al. 2014 J. Exp. Biol.

Calibration using animals themselves!

Corcoran and Hedrick , 2019 eLife

Corcoran and Hedrick, 2019 eLife

3D track generation

Automated 2D -> 3D assignment

Flexible track generation options

• Allowable error

• Gaps in detections

Camera 1 Camera 2

X

Y

Z

Evangelista et al. 2017 Proc. Roy. B

What can you do with the data?

Flight parameters

• Accelerations, ground speeds, etc…

Emergence counts/Activity patterns

Interactions with turbinesX

Y

Z

Funding:

Hopeful release date spring 2020 Presentation availablewww.sonarjamming.com

@AaronJCorcoran